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- PDB-1rhb: WATER DEPENDENT DOMAIN MOTION AND FLEXIBILITY IN RIBONUCLEASE A A... -

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Basic information

Entry
Database: PDB / ID: 1rhb
TitleWATER DEPENDENT DOMAIN MOTION AND FLEXIBILITY IN RIBONUCLEASE A AND THE INVARIANT FEATURES IN ITS HYDRATION SHELL. AN X-RAY STUDY OF TWO LOW HUMIDITY CRYSTAL FORMS OF THE ENZYME
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE (NUCLEIC ACID / RNA)
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsRadha Kishan, K.V. / Chandra, N.R. / Sudarsanakumar, C. / Suguna, K. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Water-dependent domain motion and flexibility in ribonuclease A and the invariant features in its hydration shell. An X-ray study of two low-humidity crystal forms of the enzyme.
Authors: Kishan, R.V. / Chandra, N.R. / Sudarsanakumar, C. / Suguna, K. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content
Authors: Madhusudan / Kodandapani, R. / Vijayan, M.
#2: Journal: Curr.Sci. / Year: 1991
Title: Rigid and Flexible Regions in Lysozyme and the Invariant Features in its Hydration Shell
Authors: Madhusudan / Vijayan, M.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: Crystal Structure of Low Humidity Tetragonal Lysozyme at at 2.1 Angstroms Resolution; Variability in Hydration Shell and its Structural Consequences
Authors: Kodandapani, R. / Suresh, C.G. / Vijayan, M.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1985
Title: Water-Mediated Transformations in Protein Crystals
Authors: Salunke, D.M. / Veerapandian, B. / Kodandapani, R. / Vijayan, M.
#5: Journal: Curr.Sci. / Year: 1984
Title: Water-Mediated Structural Transformations in a New Crystal Form of Ribonuclease A and Tetragonal Lysozyme
Authors: Salunke, D.M. / Veerapandian, B. / Vijayan, M.
History
DepositionNov 13, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE A


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.740, 38.250, 52.400
Angle α, β, γ (deg.)90.00, 112.66, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 93 / 2: CIS PROLINE - PRO 114

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Components

#1: Protein RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line: S2 / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 %protein11
250 %ethanol11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Num. obs: 15874 / Num. measured all: 35813 / Rmerge(I) obs: 0.047

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.5→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.173 15326
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 0 160 1107
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.0050.02
X-RAY DIFFRACTIONp_singtor_nbd0.1640.5
X-RAY DIFFRACTIONp_multtor_nbd0.2880.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1780.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.45
X-RAY DIFFRACTIONp_staggered_tor16.520
X-RAY DIFFRACTIONp_orthonormal_tor18.420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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